Merge branch 'master' of github.com:jamesagnew/hapi-fhir

hapi-fhir-base-example-embedded-ws/pom.xml

@@ -0,0 +1,47 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-fhir</artifactId>
+		<version>1.2</version>
+	</parent>
+
+	<packaging>jar</packaging>
+
+	<artifactId>hapi-fhir-base-example-embedded-ws</artifactId>
+	<dependencies>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-servlet</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-webapp</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.google.inject</groupId>
+			<artifactId>guice</artifactId>
+			<version>3.0</version>
+		</dependency>
+		<dependency>
+			<groupId>com.google.inject.extensions</groupId>
+			<artifactId>guice-servlet</artifactId>
+			<version>3.0</version>
+		</dependency>
+		<dependency>
+			<groupId>com.sun.jersey.contribs</groupId>
+			<artifactId>jersey-guice</artifactId>
+			<version>1.18.1</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dstu2</artifactId>
+			<version>1.2</version>
+		</dependency>
+	</dependencies>
+</project>

hapi-fhir-base-example-embedded-ws/src/main/java/embedded/ContextListener.java

@@ -0,0 +1,37 @@
+package embedded;
+import java.util.Map;
+
+import com.google.common.base.Joiner;
+import com.google.common.collect.ImmutableMap;
+import com.google.inject.Guice;
+import com.google.inject.Injector;
+import com.google.inject.servlet.GuiceServletContextListener;
+import com.sun.jersey.api.container.filter.GZIPContentEncodingFilter;
+import com.sun.jersey.api.core.ResourceConfig;
+import com.sun.jersey.guice.JerseyServletModule;
+
+import filters.CharsetResponseFilter;
+import filters.CorsResponseFilter;
+
+public class ContextListener extends GuiceServletContextListener {
+
+	@Override
+	protected Injector getInjector() {
+
+		return Guice.createInjector(new JerseyServletModule() {
+
+			@Override
+			protected void configureServlets() {
+				final Map<String, String> params = ImmutableMap
+						.<String, String> builder()
+						.put(ResourceConfig.PROPERTY_CONTAINER_RESPONSE_FILTERS,
+								Joiner.on(";").join(
+										CharsetResponseFilter.class.getName(),
+										CorsResponseFilter.class.getName(),
+										GZIPContentEncodingFilter.class
+												.getName())).build();
+				serve("/model/*").with(FhirRestfulServlet.class, params);
+			}
+		});
+	}
+}

hapi-fhir-base-example-embedded-ws/src/main/java/embedded/FhirRestfulServlet.java

@@ -0,0 +1,59 @@
+package embedded;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.inject.Singleton;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
+import ca.uhn.fhir.narrative.INarrativeGenerator;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
+
+@Singleton
+public class FhirRestfulServlet extends RestfulServer {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -3931111342737918913L;
+
+	public FhirRestfulServlet() {
+		super(FhirContext.forDstu2()); // Support DSTU2
+	}
+
+	/**
+	 * This method is called automatically when the servlet is initializing.
+	 */
+	@Override
+	public void initialize() {
+		/*
+		 * Two resource providers are defined. Each one handles a specific type
+		 * of resource.
+		 */
+		final List<IResourceProvider> providers = new ArrayList<IResourceProvider>();
+		providers.add(new SomeResourceProvider());
+		setResourceProviders(providers);
+
+		/*
+		 * Use a narrative generator. This is a completely optional step, but
+		 * can be useful as it causes HAPI to generate narratives for resources
+		 * which don't otherwise have one.
+		 */
+		final INarrativeGenerator narrativeGen = new DefaultThymeleafNarrativeGenerator();
+		getFhirContext().setNarrativeGenerator(narrativeGen);
+
+		/*
+		 * Tells HAPI to use content types which are not technically FHIR
+		 * compliant when a browser is detected as the requesting client. This
+		 * prevents browsers from trying to download resource responses instead
+		 * of displaying them inline which can be handy for troubleshooting.
+		 */
+		setUseBrowserFriendlyContentTypes(true);
+
+		registerInterceptor(new ResponseHighlighterInterceptor());
+
+	}
+}

hapi-fhir-base-example-embedded-ws/src/main/java/embedded/ServerStartup.java

@@ -0,0 +1,25 @@
+package embedded;
+import java.util.EnumSet;
+
+import javax.servlet.DispatcherType;
+
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.DefaultServlet;
+import org.eclipse.jetty.servlet.ServletContextHandler;
+
+import com.google.inject.servlet.GuiceFilter;
+
+public class ServerStartup {
+
+	public static void main(final String[] args) throws Exception {
+
+		final Server server = new Server(9090);
+		final ServletContextHandler sch = new ServletContextHandler(server, "/");
+		sch.addEventListener(new ContextListener());
+		sch.addFilter(GuiceFilter.class, "/*",
+				EnumSet.of(DispatcherType.REQUEST));
+		sch.addServlet(DefaultServlet.class, "/");
+		server.start(); 
+	}
+
+}

hapi-fhir-base-example-embedded-ws/src/main/java/embedded/SomeResourceProvider.java

@@ -0,0 +1,28 @@
+package embedded;
+
+import java.util.List;
+
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import ca.uhn.fhir.model.dstu2.resource.Practitioner;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.rest.annotation.RequiredParam;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+
+public class SomeResourceProvider implements IResourceProvider {
+
+	@Override
+	public Class<? extends IBaseResource> getResourceType() {
+		return Practitioner.class;
+	}
+
+	@Search()
+	public List<Practitioner> findPractitionersByName(
+			@RequiredParam(name = Practitioner.SP_NAME) final StringDt theName) {
+		throw new UnprocessableEntityException(
+				"Please provide more than 4 characters for the name");
+	}
+
+}

hapi-fhir-base-example-embedded-ws/src/main/java/filters/CharsetResponseFilter.java

@@ -0,0 +1,24 @@
+package filters;
+
+
+import javax.ws.rs.core.HttpHeaders;
+import javax.ws.rs.core.MediaType;
+
+import com.sun.jersey.spi.container.ContainerRequest;
+import com.sun.jersey.spi.container.ContainerResponse;
+import com.sun.jersey.spi.container.ContainerResponseFilter;
+
+public class CharsetResponseFilter implements ContainerResponseFilter {
+
+	@Override
+	public ContainerResponse filter(final ContainerRequest request,
+			final ContainerResponse response) {
+
+		final MediaType contentType = response.getMediaType();
+		if (contentType != null) {
+			response.getHttpHeaders().putSingle(HttpHeaders.CONTENT_TYPE,
+					contentType.toString() + ";charset=UTF-8");
+		}
+		return response;
+	}
+}

hapi-fhir-base-example-embedded-ws/src/main/java/filters/CorsResponseFilter.java

@@ -0,0 +1,33 @@
+package filters;
+
+
+import javax.ws.rs.core.Response;
+import javax.ws.rs.core.Response.ResponseBuilder;
+
+import com.sun.jersey.spi.container.ContainerRequest;
+import com.sun.jersey.spi.container.ContainerResponse;
+import com.sun.jersey.spi.container.ContainerResponseFilter;
+
+public class CorsResponseFilter implements ContainerResponseFilter {
+
+	@Override
+	public ContainerResponse filter(final ContainerRequest req,
+			final ContainerResponse contResp) {
+
+		final ResponseBuilder resp = Response.fromResponse(contResp
+				.getResponse());
+		resp.header("Access-Control-Allow-Origin", "*").header(
+				"Access-Control-Allow-Methods", "GET, POST, OPTIONS");
+
+		final String reqHead = req
+				.getHeaderValue("Access-Control-Request-Headers");
+
+		if (null != reqHead && !reqHead.equals("")) {
+			resp.header("Access-Control-Allow-Headers", reqHead);
+		}
+
+		contResp.setResponse(resp.build());
+		return contResp;
+	}
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/ReadMethodBinding.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.rest.method;
 
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -138,6 +140,9 @@ public class ReadMethodBinding extends BaseResourceReturningMethodBinding implem
 				return false;
 			}
 		}
+		if (isNotBlank(theRequest.getCompartmentName())) {
+			return false;
+		}
 		if (theRequest.getRequestType() != RequestTypeEnum.GET) {
 			ourLog.trace("Method {} doesn't match because request type is not GET: {}", theRequest.getId(), theRequest.getRequestType());
 			return false;
@@ -198,6 +203,9 @@ public class ReadMethodBinding extends BaseResourceReturningMethodBinding implem
 			return resource;
 		case BUNDLE_PROVIDER:
 			return new SimpleBundleProvider(resource);
+		case BUNDLE_RESOURCE:
+		case METHOD_OUTCOME:
+			break;
 		}
 
 		throw new IllegalStateException("" + getMethodReturnType()); // should not happen

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamString.java

@@ -43,6 +43,9 @@ import org.hibernate.search.annotations.Field;
 })
 public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchParam {
 
+	/*
+	 * Note that MYSQL chokes on unique indexes for lengths > 255 so be careful here 
+	 */
 	public static final int MAX_LENGTH = 200;
 
 	private static final long serialVersionUID = 1L;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamUri.java

@@ -43,7 +43,10 @@ import org.hibernate.search.annotations.Indexed;
 //@formatter:on
 public class ResourceIndexedSearchParamUri extends BaseResourceIndexedSearchParam {
 
-	public static final int MAX_LENGTH = 256;
+	/*
+	 * Note that MYSQL chokes on unique indexes for lengths > 255 so be careful here 
+	 */
+	public static final int MAX_LENGTH = 255;
 
 	private static final long serialVersionUID = 1L;
 

hapi-fhir-osgi-core/pom.xml

@@ -167,23 +167,23 @@
 			</resource>
 			<resource>
 				<directory>../hapi-fhir-structures-dstu/src/main/resources</directory>
-				<filtering>true</filtering>
+				<filtering>false</filtering>
 			</resource>
 			<resource>
 				<directory>../hapi-fhir-structures-dstu/target/generated-resources/tinder</directory>
-				<filtering>true</filtering>
+				<filtering>false</filtering>
 			</resource>
 			<resource>
 				<directory>../hapi-fhir-structures-dstu2/src/main/resources</directory>
-				<filtering>true</filtering>
+				<filtering>false</filtering>
 			</resource>
 			<resource>
 				<directory>../hapi-fhir-structures-dstu2/target/generated-resources/tinder</directory>
-				<filtering>true</filtering>
+				<filtering>false</filtering>
 			</resource>
 			<resource>
 				<directory>../hapi-fhir-structures-hl7org-dstu2/src/resources/java</directory>
-				<filtering>true</filtering>
+				<filtering>false</filtering>
 			</resource>
 		</resources>
 	</build>

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/CompartmentDstu2Test.java

@@ -0,0 +1,187 @@
+package ca.uhn.fhir.rest.server;
+
+import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.startsWith;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.ContentType;
+import org.apache.http.entity.StringEntity;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.dstu2.resource.Encounter;
+import ca.uhn.fhir.model.dstu2.resource.Observation;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
+import ca.uhn.fhir.rest.annotation.Create;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.OptionalParam;
+import ca.uhn.fhir.rest.annotation.Read;
+import ca.uhn.fhir.rest.annotation.ResourceParam;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.util.PortUtil;
+
+/**
+ * Created by dsotnikov on 2/25/2014.
+ */
+public class CompartmentDstu2Test {
+	private static CloseableHttpClient ourClient;
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CompartmentDstu2Test.class);
+	private static int ourPort;
+	private static Server ourServer;
+	private static String ourLastMethod;
+	private static FhirContext ourCtx = FhirContext.forDstu2();
+	private static IdDt ourLastId;
+
+	@Before
+	public void before() {
+		ourLastMethod = null;
+		ourLastId = null;
+	}
+
+
+	@Test
+	public void testReadFirst() throws Exception {
+		init(new TempPatientResourceProvider());
+		
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/123");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+		ourLog.info("Response was:\n{}", responseContent);
+		assertEquals("read", ourLastMethod);
+		assertEquals("Patient", ourLastId.getResourceType());
+		assertEquals("123", ourLastId.getIdPart());
+		assertThat(responseContent, startsWith("<Patient"));
+	}
+
+	@Test
+	public void testCompartmentSecond() throws Exception {
+		init(new TempPatientResourceProvider());
+		
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/123/Encounter");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+		ourLog.info("Response was:\n{}", responseContent);
+		assertEquals("searchEncounterCompartment", ourLastMethod);
+		assertEquals("Patient", ourLastId.getResourceType());
+		assertEquals("123", ourLastId.getIdPart());
+		assertThat(responseContent, startsWith("<Bundle"));
+		assertThat(responseContent, containsString("<Encounter"));
+	}
+
+	@Test
+	public void testCompartmentSecond2() throws Exception {
+		init(new TempPatientResourceProvider());
+		
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/123/Observation");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+		ourLog.info("Response was:\n{}", responseContent);
+		assertEquals("searchObservationCompartment", ourLastMethod);
+		assertEquals("Patient", ourLastId.getResourceType());
+		assertEquals("123", ourLastId.getIdPart());
+		assertThat(responseContent, startsWith("<Bundle"));
+		assertThat(responseContent, containsString("<Observation"));
+	}
+
+	@After
+	public void after() throws Exception {
+		ourServer.stop();
+		ourClient.close();
+	}
+
+	public void init(IResourceProvider... theProviders) throws Exception {
+		ourPort = PortUtil.findFreePort();
+		ourServer = new Server(ourPort);
+
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer(ourCtx);
+		servlet.setResourceProviders(theProviders);
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+	}
+
+	public static class TempPatientResourceProvider implements IResourceProvider {
+		@Override
+		public Class<Patient> getResourceType() {
+			return Patient.class;
+		}
+
+		@Read()
+		public Patient method1Read(final @IdParam IdDt theId) {
+			ourLastMethod = "read";
+			ourLastId = theId;
+			Patient patient = new Patient();
+			patient.setId(theId);
+			return patient;
+		}
+
+		@Search(compartmentName = "Encounter")
+		public List<Encounter> method2SearchCompartment(final @IdParam IdDt theId) {
+			ourLastId = theId;
+			ourLastMethod = "searchEncounterCompartment";
+			System.out.println("Encounter compartment search");
+			List<Encounter> encounters = new ArrayList<Encounter>();
+			Encounter encounter = new Encounter();
+			encounter.setId("1");
+			encounter.setPatient(new ResourceReferenceDt(theId));
+			encounters.add(encounter);
+			return encounters;
+		}
+
+		@Search(compartmentName = "Observation")
+		public List<Observation> method2SearchCompartment2(final @IdParam IdDt theId) {
+			ourLastId = theId;
+			ourLastMethod = "searchObservationCompartment";
+			System.out.println("Encounter compartment search");
+			List<Observation> encounters = new ArrayList<Observation>();
+			Observation obs = new Observation();
+			obs.setId("1");
+			obs.setSubject(new ResourceReferenceDt(theId));
+			encounters.add(obs);
+			return encounters;
+		}
+
+	}
+
+}

hapi-fhir-testpage-overlay/src/main/java/ca/uhn/fhir/to/TesterConfig.java

@@ -27,6 +27,7 @@ public class TesterConfig {
 
 	public IServerBuilderStep1 addServer() {
 		ServerBuilder retVal = new ServerBuilder();
+		myServerBuilders.add(retVal);
 		return retVal;
 	}
 

pom.xml

@@ -190,6 +190,10 @@
 			<id>botunge</id>
 			<name>Thomas Andersen</name>
 		</developer>
+		<developer>
+			<id>samlanfranchi</id>
+			<name>Sam Lanfranchi</name>
+		</developer>
 	</developers>
 
 	<licenses>
@@ -1374,4 +1378,7 @@
 		</profile>
 	</profiles>
 
+	<modules>
+		<module>hapi-fhir-base-example-embedded-ws</module>
+	</modules>
 </project>

src/changes/changes.xml

@@ -194,6 +194,19 @@
 				handle JSON responses or use interceptors. Thanks to
 				JT for reporting!
 			</action>
+			<action type="add">
+				JPA server maximumn length for a URI search parameter has been reduced from
+				256 to 255 in order to accomodate MySQL's indexing requirements
+			</action>
+			<action type="fix" issue="242">
+				Server failed to respond correctly to compartment search operations
+				if the same provider also contained a read operation. Thanks to GitHub user
+				@am202 for reporting!
+			</action>
+			<action type="fix" issue="245">
+				FIx issue in testpage-overlay's new Java configuration where only the first
+				configured server actually gets used.
+			</action>
 		</release>
 		<release version="1.2" date="2015-09-18">
 			<action type="add">

vagrant/Vagrantfile

@@ -86,7 +86,7 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
 				proxy_port: 80,
 				# ssl_port: 443,
 				authbind: 'yes',
-				java_options: '-Dfhir.logdir=/var/log/fhir -Dfhir.db.location=/var/fhirdb'
+				java_options: '-Dfhir.logdir=/var/log/fhir -Dfhir.db.location=/var/fhirdb -Dfhir.db.location.dstu2=/var/fhirdb2 -Dfhir.lucene.location.dstu2=/var/fhirlucene2'
 			},
 			mysql: {
 				version: '5.6',